Faecal Microbial Analysis – A guide to heal my gut

Faecal Microbial Analysis – how the report will help me heal my gut.

Remission from daily stomach pain and ulcerative colitis has been a hard won victory for me, but it was undone in a mouthful. A family holiday to Vietnam earlier this year brought back a world of familiar tummy pain.

Who knows what I ate? On the 3rd day whilst my family frolicked on the beach, I lay low and kept desperately close to the loo. It was only a 24 hour thing but it impacted me for weeks with constipation and diarrhoea, painful bloating and continual stomach tenderness. These are common digestive upsets that indicate something is out of balance. It was time to investigate further.

I felt sure I had a parasite. That would have been the simplest explanation. Back home, tests came back negative. My gut had a history of being more complex than that.

I had been keen to have a Bioscreen, Faecal Microbial Analysis (FMA) for years but the price had always discouraged me. Actually, to be honest, I thought I was all good without it. Intellectually, I new what was required for gut health; ‘A Gut Feeling’ had me on top of the news. I’d changed my diet dramatically already, I’d done years of gut healing with significant results. I’d been in remission from ulcerative colitis for 3 years. Until this traveler’s hiccup, I actually thought I was doing ok, microbially that is.

Why I wanted to know what was actually living inside my gut.

I’m damn curious. (Parasites and poo are a dinner table favourite). No, seriously, I had a lot of questions….. I’d struggled with IBS and colitis for 20 years. Did I have an abundance of bad bacteria? Could this explain why my symptoms seemed to never fully resolve, or at least, came back so quickly? I’d taken a truck load of antibiotics in my life and been a total sugar addict!

So what is a Faecal Microbial Analysis?

FMA is a specialist stool test that investigates the microscopic gut flora of the lower intestinal tract. It cultures and counts the bacteria that should be in your gut. The test measures aerobes and anaerobes, 2 significant bacteria groups (read about them here) plus the yeast living in the colon.

It is different to the common stool tests from your GP (faecal bacteriology and parasitology tests) which check for abnormal bacteria and parasites that shouldn’t be in your gut. This is what I’d had to check for parasites.

The analysis provides quantitative data on microbial strains and shows imbalances between what is known to be good and bad in your intestinal ecosystem. An impressive 5000 organisms are screened, however, only a small fraction of these are likely to be hanging out in your gut and end up on the report.

It’s all about balance.

The ratio of good to bad bacteria is not only a critical measure in determining your gut health but your overall health! An ideal balance is about 85 percent good and 15 percent bad. And, It’s not necessarily the presence or absence of one particular type of bacteria that makes for a healthy microbiome. Diversity is the key.

In very basic terms, here’s summary of my report:

Bad, disease causing bacteria.

I didn’t have any?

So, I didn’t have an overgrowth of pathogenic bacteria (the seriously bad guys) A part of me was a bit disappointed. I was ready for a fight. I like to name and blame!

Pathogenic disease causing bacteria (H.pylori or clostrifium difficile for eg) or yeast (candida) can stop beneficial bacteria from thriving and in turn effect the proper functioning of your whole body. It’s also important to note that an overgrowth of a beneficial bacteria can cause problems as well. As I said, it’s all about balance.

The good guys. The health promoting bacteria.

I didn’t have any!!!

Oh know. I didn’t expect this news. Years of healing and eating fermented food had not improved my gut flora at all. Clearly I am leaking!!!

No good guys? What does that mean? Ok, I’m exaggerating. I did have a few meagre bacteroides, lactobacilli and Bifidobacterium but they were in alarmingly low numbers. My ‘diversity’ was pretty narrow.

Where is all the good bacteria I eat going?

It’s probably just dying off like seeds in poor soil without regular water. The report has made it obvious that my gut flora is out of balance and in poorer shape than I thought.

This is evidence enough that I have leaky gut. I’d suspected this much for years but never imagined it could be so bad.

The most important thing I learnt about my gut flora.

I have a low and limited distribution of Bacteroides. This is a big problem and may be the key to my healing.

Bacteroides make up approximately a third of total gut flora. Humans became inoculated with bacteroides during the birth process and then through breast milk. After that, its lifestyle and diet that determines their survival – they need to be fed well to proliferate. Unlike other gut bacteria they can’t be grown (fermentated foods) or made into a probiotic. Bacteroides cannot exist outside the human gut; oxygen kills bacteroides quickly. Interestingly, the absence of bacteroides can result in serious bowel pathology. Could this may explain my ulcerative colitis??

It was suggested that low Bacteroides levels could be inhibiting other necessary strains of bacteria from flourishing.

I make homemade, 24 hour yoghurt that is full of lactobacilli. I have eaten a cup every day for nearly 3 years. I also take a probiotic with lactobacilli. Despite this, my report indicates an undergrowth of lactobacilli?? Eating more yoghurt is probably not the answer; however increasing my Bacteroide community may improve the conditions for lactobacilli to thrive? Sounds like a good experiment. The report has given me some tips on how to do this. As I said, Bacteroides are not found in a probiotic, they benefit from a bit of dedication and time in your home kitchen.

Every summary report will be different. These are the recommendations I was given:

For Low Bacteroides:

“The intake of fructo-oligosaccharides (FOS) may assist.” In other words eat diverse prebiotic foods such as vegetables, nuts and seeds.

“A general diet consisting of meat/bone broth, fish or soybean protein may assist the growth of these organisms”. If numbers of bacteroides are low then meat and meat broth provides essential building block nutrients. (source) It was recommended that I build up to at least 3 cups of bone broth a day.

“Consider the supplement of vitamin K2 to improve the growth of anaerobes. A high concentration of K2 is found in natural yoghurt, cheese and butter”.

“Consider the supplement of biotin to assist the production of fatty acids by anaerobes”. (Apple cider vinegar before meals will do this)

For low Bifidobacterium and lactobacilli sp.

“Oral probiotic supplementation may be beneficial”. It was suggested by my GP to increase lactobacilli Rhamnosus.

So it’s back to the brothery and fermented kitchen for me. I will drink broth far more than I have EVER …… more than I can possibly stomach perhaps.

The test has been a window into one small fraction of my unknown yet super important microbiome. These unexpected results are my motivation to go for broke when it comes to microbial multiculturalism. Fortunately this little world is continually shape shifting. Nothing is fixed or permanent in there. I can make bone broth, I can supplement more and I can eat more fermented foods. As with any ecosystem, it’s the community as a whole that matters. Their proliferation is going to have to start in my kitchen. I’m going to have to get busy catering for a healthy bacteria party in my gut.

Faecal Microbial Analysis – A guide to heal my gut – Is it worth the money?

$350. I think so. A sensitive gut is a forever nuisance! The results make me more determined to heal and seal. I long for the day that I can travel and eat out without fearing damage and discomfort. Some direction is helpful.

Where to get tested and how to read the report.

I had may test done by Bioscreen in melbourne. I am not affiliated with this lab. A word of advice, the report is quite tricky to interpret and uses medical terms that may need googling. It’s advisable to spend some time going through it with your GP or health guide. Like me, you will probably have loads of questions?

I’d love to hear if you have found the test worthwhile.

I can see a future when analysis of your microbiome will one day be as common as routine blood tests. Doctors could discuss results with you and the management of your gut bacteria as the foundation for your overall health plan.

Comments

I have only recently come across your blog while googling gut flora. Fabulous site. Your article on your faecal test was inzpiring. I have been looking into my gut biome lately as to how it affects my blood sugar levels (t2 diabetes). I have suffered from constipation practically all my life and now realise it is dow to my poor diet which is starving my gut baceria.

Thanks for commenting. I appreciate it. Good luck with your gut journey. I’m not up with T2 diabetes but like every modern health condition, I’m sure it will have awesome benefits. Let me know if the test is valuable for you. I’m sipping a broth as I write. Take care

Recently has the bioscreen done. Major overgrowth of the baddies streptococcus, enterococcus, cdiff. Undergrowth of all the beneficial bacteria and even undetected levels of E.coli. History: ‘slow transit constipation’ (8-9 days without going). Occasionally opposite reaction. I guess constipated-predominant IBS. Chronic fatigue syndrome, gradually worsening over time to sometimes being out cold for max 40 hours. Lyme disease. 31yo female, two children. Chronic illness for 15 years since after birth of first child. My doctor said it is ESSENTIAL to treat the gut before attacking the Lyme. And says strep over growth is commonly associated with Chronic Fatigue syndrome. I strongly encourage anyone with ongoing health issues to get the faecal microbial analysis done. Worth every dollar. ? due to the overgrowth of pathogens I’ve had to commence on a long regime including specific antibiotics to kill them off, prescription probiotics to build up the undergrowth of good bacteria. And other supplements and diet regime. Bone broth ++ 2 weeks into treatment I have ALREADY started going most days which I have NEVER done. Has always been once a week then worsened as my health did.

yes WOW, you have discovered a lot of things from this test. I’m glad you’ve found it helpful because I can imagine by your symptoms you have felt quite desperate (not just crappy). Stay in touch and let me know how you’re fairing over time. Amazing to hear you noticed improvements in just 2 weeks. So encouraging. Thanks for sharing your story. Take care xx

Hi Sharne, Thank you for your interest. I’ve been very well – prob better than I have in years. I’ve been able to reintroduce once problematic foods (like garlic and onion) which is very exciting and tasty. I have, however just spent 3 weeks in Thailand where I (not by choice) was exposed to traces of gluten, trans fats, MSG and loads of unnecessary sugar in most meals. This has set me back a bit and I’m keen to return to my strict healing regime which I know works for me and my tummy woes. Good luck with your daughter. Keep in touch. Let me know how she goes for others to benefit. Take care

Wow, I have such a long way to go to heal my gut, this is a great platform to start learning
what to avoid, what to eat, how to start healing from the inside out, Thank you for putting
this blog out there.
God bless You 🙂

A GAPS practitioner could help you. Here is a link to GAPS Australia. These doctors will be trained in reading stool analysis results and hopefully will understand histamine intolerance as well. Full GAPS is very manageable but stage one GAPS is hard core. I wish you the best of luck and hope you can find a gut savy practitioner in your area to help you.

I think it’s serendipitous that I found your blog today. I’m 24 years old and my gut problems began about 3 years ago. I recently was traveling abroad and got food poisoning on my last day. Now, two weeks later, and I still have terrible symptoms. I talked to my doctor today who said to up my probiotic intake, make sure to take psyllium daily, and also take pepto bismol. If that doesn’t get me back to normal, stool sample it is. Thank you for sharing your insight, I’m finding comfort in knowing I’m not the only one with issues like these. Hugs from California!

Hi California friend. Thanks for taking the time to post. Sorry to hear about your tummy after travelling. Yes, it’s certainly nice to know you’re not alone. I promise there are millions of people like us!!! It is very common to have ongoing stomach issues after traveling. Let us know how you go. good luck

Thanks for your great site! I did the bioscreen test last year and have revisited it because I am still so unwell and getting worse. Can hardly eat much and have gained 25 kg 🙁
My results show an overgrowth of ‘bad guys’ and Cellulolytic Bacteroides sp. : Undetected
Given that I read bactericides are usually 30% of the gut bacteria it does seem a worry that i have none! Would love to hear from anyone who has successfully treated severe dysbiosis. And yes, in the future I am sure more will pay attention to this vital information. I wish you all wellness!

Hi, thanks for you message. Sorry to hear you are still unwell and feel you are getting worse. It’s a tricky path. When you said you are going to revisit Bioscreen – do you mean you want to retest? If you are can I suggest a different company? I haven’t yet had this test done my self but I have been in contact with them and they claim, to have more advanced technology and can detect a far greater number of microbial species. They also personally help with diet and give advice as to how to build up species where you need. Here is their link. The website is not easy to navigate – but I hope this help you or some one elsehttp://tagc.com.au/gut/gut-microbiome/

I am a 57 year old male who has been diagnosed with an auto immune disease about 8 years ago. I was in a high profile government position which came with significant stress.
I have seen two rheumatologist in Melbourne with really little improvement. I have been on a range of drugs daily from the first visit to the doctors.

I have been told that it may be Polymyalgia and then some time later it was decided that I could have Ankylosing Spondylitis. The Rheumatologists were honest and have said we are not sure of the exact condition but we will treat you as if you have these diseases.

After a recent visit to a physio who had some personal experience with AS he said that he had had a lot of success with a Dr Nastasi in Doncaster. The physio recommended that the first thing I do is get an FMA test which is about $360. This takes about 4 weeks to process and then I will go along to see Dr Nastasi.

I’ve only recently started to read about the gut. Currently reading the Inside Story. I have also looked at your recipes and I am about to try the anti inflammatory smoothies. I guess the real reason for this email is to see if you believe that having yet another test (FMA) and exploring if their is a link between autoimmune and the gut.
That is, should I ring up and order a Bioscreen FMA kit and then go along and see yet another doctor ? I have literally spent thousands over the last few years and it seems that all the Rheumatologists will do is try different drugs. Very little mention of diet and the zero about the gut. I have had no improvement and in fact feel worse.

Hi Peter, I apologise for the long wait for my reply. I’ve been away for a few weeks. I’m not a practitioner but I do believe that auto immunity is connected to the gut and the more you can know about your gut the better. I would actually recommend a FMA test via ‘SMART GUT’ – google ‘SMART DNA’ I have dome both but I believe this one is more comprehensive. I have a post on this test on my blog too. A good naturopath who understands your conditions is also important. Smart gut will recommend someone in your area. They are also trained in reading the analysis. Significant dietary changes will be required. Your micro biome is a consequence of the food you eat! Good luck – I sincerely hope you find some answers.

Just wanted to say thanks for posting this blog – it was the thing that helped me solve my health issue that had been plaguing me for a number of years. I had IBS, fatigue, low iron, skin issues, no period, pain etc. I’d been following FODMAP and seen a little bit of improvement but still tired. I’d seen my GP, Specialists, had a colonoscopy, seen a dietian, nutritionist, everyone. And then after reading this I went had a CSTA with a ‘functional medicine clinic’ aka nuturopath and discovered I had system wide Candida infection that was causing all of this. Fast forward 6 months of eating a Candida killing diet and I feel like a new woman! Thanks so much for this – it really did change my life for the better.